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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ), 'gf_id' => 'HOM05D001353', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001353' ), 'data_identifier' => 'HOM05D001353', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001353', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '464', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37890' => 'bna', 'A03p34610' => 'bna', 'A03p39730' => 'bna', 'A07p00600' => 'bna', 'Aa31LG5G16790' => 'aar', 'Aa31LG8G17000' => 'aar', 'Aa31LG8G3360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5585' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2049' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.659' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.691' => 'aag', 'Actinidia09438' => 'ach', 'Actinidia20405' => 'ach', 'Actinidia21695' => 'ach', 'Actinidia23458' => 'ach', 'Actinidia32713' => 'ach', 'Actinidia40213' => 'ach', 'Ah.09g230830' => 'amhyb', 'Ah.13g071560' => 'amhyb', 'AL3G17160' => 'aly', 'AL3G28920' => 'aly', 'AL3G28930' => 'aly', 'AL3G48050' => 'aly', 'Aqoxy2G03190' => 'aox', 'Aqoxy5G00563' => 'aox', 'Aqoxy7G01509' => 'aox', 'Aqoxy7G01510' => 'aox', 'Aqoxy7G03127' => 'aox', 'arahy.Tifrunner.gnm1.ann1.8T8ZNV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CH6KF4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I5K3IU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K0TTLC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYDP5Z' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YNQ283' => 'arhy', 'AT2G20050' => 'ath', 'AT3G06270' => 'ath', 'AT3G16220' => 'ath', 'AT3G16230' => 'ath', 'ATR0315G016' => 'atr', 'ATR0315G080' => 'atr', 'ATR0315G092' => 'atr', 'ATR0315G123' => 'atr', 'ATR0626G385' => 'atr', 'Atru.chr1.3457' => 'acertr', 'Atru.chr1.3463' => 'acertr', 'Atru.chr4.2698' => 'acertr', 'Atru.chr7.1420' => 'acertr', 'AUR62010934' => 'cqu', 'AUR62021446' => 'cqu', 'AUR62022162' => 'cqu', 'AUR62031870' => 'cqu', 'AUR62040380' => 'cqu', 'AUR62040725' => 'cqu', 'BcaB03g14667' => 'bca', 'BcaB03g16799' => 'bca', 'BcaB04g18890' => 'bca', 'BcaB04g21326' => 'bca', 'BcaC01g03832' => 'bca', 'BcaC01g03834' => 'bca', 'BcaC01g03835' => 'bca', 'BcaC05g30041' => 'bca', 'BcaC06g36681' => 'bca', 'BcaC09g47880' => 'bca', 'BcaC09g47881' => 'bca', 'BcaC09g48591' => 'bca', 'BcaC09g48592' => 'bca', 'BcaC09g48593' => 'bca', 'BNapus_Darmor_BZH_scaffold_118p00240' => 'bna', 'BolC1t05631H' => 'bol', 'BolC1t05633H' => 'bol', 'BolC3t16487H' => 'bol', 'BolC3t17020H' => 'bol', 'BolC3t17094H' => 'bol', 'BolC3t17095H' => 'bol', 'BolC7t40548H' => 'bol', 'BraA01t03849Z' => 'bra', 'BraA01t04446Z' => 'bra', 'BraA01t04448Z' => 'bra', 'BraA03t12637Z' => 'bra', 'BraA03t13120Z' => 'bra', 'BraA03t13123Z' => 'bra', 'BraA07t27856Z' => 'bra', 'C01p48010' => 'bna', 'C03p42070' => 'bna', 'C03p48160' => 'bna', 'C03p48170' => 'bna', 'C07p01090' => 'bna', 'CAN.G206.170' => 'can', 'CAN.G438.39' => 'can', 'CAN.G60.8' => 'can', 'CAN.G889.14' => 'can', 'CANSAT56G0514' => 'cansat', 'CANSAT56G3175' => 'cansat', 'CANSAT78G0472' => 'cansat', 'CARHR080790' => 'chi', 'CARHR091410' => 'chi', 'CARHR091420' => 'chi', 'CARHR110520' => 'chi', 'Carub.0003s0570' => 'cru', 'Carub.0003s1597' => 'cru', 'Carub.0003s1598' => 'cru', 'Carub.0003s3431' => 'cru', 'Ca_00592_v3' => 'car', 'Ca_01153_v3' => 'car', 'Ca_25556_v3' => 'car', 'CBR_g20332' => 'cbr', 'CBR_g34538' => 'cbr', 'CBR_g48193' => 'cbr', 'CBR_g9064' => 'cbr', 'Cc03_g02780' => 'ccan', 'Cc04_g02860' => 'ccan', 'Cc06_g10150' => 'ccan', 'CDE01G0312' => 'cde', 'CDE01G0434' => 'cde', 'CDE05G1729' => 'cde', 'CDE05G3143' => 'cde', 'CDE05G3629' => 'cde', 'CDE12G0565' => 'cde', 'Cfa002108' => 'cfa', 'Cfa003217' => 'cfa', 'Cfa022620' => 'cfa', 'Cfa023308' => 'cfa', 'Ciclev10005047m.g' => 'ccl', 'Ciclev10007299m.g' => 'ccl', 'Ciclev10025383m.g' => 'ccl', 'CiPaw.01G156900' => 'cil', 'CiPaw.01G234100' => 'cil', 'CiPaw.02G089700' => 'cil', 'CiPaw.03G227500' => 'cil', 'ClCG05G005550' => 'cla', 'ClCG06G005630' => 'cla', 'ClCG06G008930' => 'cla', 'ClCG09G001840' => 'cla', 'COL.COLO4_13974' => 'col', 'COL.COLO4_30466' => 'col', 'COL.COLO4_34797' => 'col', 'Cpa.g.c32037' => 'cpa', 'Cpa.g.sc109.36' => 'cpa', 'Cpa.g.sc16.68' => 'cpa', 'Cpa.g.sc40.28' => 'cpa', 'Cre01.g008000' => 'cre', 'Cre10.g443550' => 'cre', 'CsaV3_1G019530' => 'csa', 'CsaV3_3G013890' => 'csa', 'CsaV3_6G005520' => 'csa', 'CsaV3_6G021270' => 'csa', 'CsaV3_7G033510' => 'csa', 'CSS0003297' => 'camsi', 'CSS0007564' => 'camsi', 'CSS0012448' => 'camsi', 'CSS0017342' => 'camsi', 'CSS0044224' => 'camsi', 'CSS0049454' => 'camsi', 'DCAR_007575' => 'dca', 'DCAR_024695' => 'dca', 'DCAR_030579' => 'dca', 'Dinv30464' => 'din', 'Dinv38354' => 'din', 'Dinv41647' => 'din', 'Dinv44458' => 'din', 'Duzib052G0364' => 'dzi', 'Duzib160G0428' => 'dzi', 'Duzib168G0382' => 'dzi', 'Duzib212G0320' => 'dzi', 'ECA247G1811' => 'eca', 'EL10Ac3g06537' => 'bvu', 'EL10Ac8g18420' => 'bvu', 'EL10Ac9g22047' => 'bvu', 'Eucgr.F03052' => 'egr', 'Eucgr.H03639' => 'egr', 'FAN02G1855' => 'fan', 'FAN02G4091' => 'fan', 'FAN05G1388' => 'fan', 'FAN07G0586' => 'fan', 'FAN07G1695' => 'fan', 'FAN12G2683' => 'fan', 'FAN12G2983' => 'fan', 'FAN12G2992' => 'fan', 'FAN14G4842' => 'fan', 'FAN17G2549' => 'fan', 'FAN19G2369' => 'fan', 'FAN19G3205' => 'fan', 'FAN22G1467' => 'fan', 'FAN23G0742' => 'fan', 'FAN26G1003' => 'fan', 'FAN26G1973' => 'fan', 'FAN28G0622' => 'fan', 'FvH4_1g05740' => 'fve', 'FvH4_4g13960' => 'fve', 'FvH4_4g23310' => 'fve', 'FvH4_6g31960' => 'fve', 'Glyma.01G146600' => 'gma', 'Glyma.07G253900' => 'gma', 'Glyma.09G194200' => 'gma', 'Glyma.13G211800' => 'gma', 'Glyma.13G355900' => 'gma', 'Glyma.15G018200' => 'gma', 'Glyma.15G100900' => 'gma', 'Glyma.17G020400' => 'gma', 'Gohir.A02G044700' => 'ghi', 'Gohir.A02G119300' => 'ghi', 'Gohir.A02G119400' => 'ghi', 'Gohir.A06G065400' => 'ghi', 'Gohir.A07G004300' => 'ghi', 'Gohir.A09G081400' => 'ghi', 'Gohir.A09G231900' => 'ghi', 'Gohir.A10G105901' => 'ghi', 'Gohir.D01G122750' => 'ghi', 'Gohir.D02G050600' => 'ghi', 'Gohir.D03G060300' => 'ghi', 'Gohir.D06G064000' => 'ghi', 'Gohir.D07G007900' => 'ghi', 'Gohir.D09G081500' => 'ghi', 'Gohir.D09G233000' => 'ghi', 'Gohir.D10G162232' => 'ghi', 'Gorai.001G007600' => 'gra', 'Gorai.001G182600' => 'gra', 'Gorai.003G064100' => 'gra', 'Gorai.005G055900' => 'gra', 'Gorai.006G097100' => 'gra', 'Gorai.006G255900' => 'gra', 'Gorai.010G074600' => 'gra', 'Gorai.011G181400' => 'gra', 'GSVIVG01015338001' => 'vvi', 'GSVIVG01017044001' => 'vvi', 'GSVIVG01017855001' => 'vvi', 'HanXRQChr04g0096261' => 'han', 'HanXRQChr04g0096271' => 'han', 'HanXRQChr07g0192671' => 'han', 'HanXRQChr16g0507681' => 'han', 'Haze_01006' => 'cav', 'Haze_16338' => 'cav', 'Haze_25790' => 'cav', 'Haze_25791' => 'cav', 'Hma1.2p1_0643F.1_g194440' => 'hma', 'Hma1.2p1_0659F.1_g197330' => 'hma', 'Hma1.2p1_0945F.1_g240170' => 'hma', 'Hma1.2p1_0945F.1_g240180' => 'hma', 'HPP92_000392' => 'vpl', 'HPP92_000452' => 'vpl', 'HPP92_005271' => 'vpl', 'HPP92_005272' => 'vpl', 'HPP92_005273' => 'vpl', 'HPP92_011802' => 'vpl', 'Hund00659' => 'sun', 'Hund20672' => 'sun', 'Lalb_Chr15g0087201' => 'lal', 'Lalb_Chr18g0055901' => 'lal', 'Lalb_Chr22g0352601' => 'lal', 'Lalb_Chr24g0396041' => 'lal', 'Lalb_Chr24g0397361' => 'lal', 'Lj2g0022100' => 'lja', 'Lj3C806G2' => 'lonja', 'Lj3g0013233' => 'lja', 'Lj4g0000925' => 'lja', 'Lj6A665G70' => 'lonja', 'Lj6g0010250' => 'lja', 'Lj7C659T6' => 'lonja', 'Lj7C659T7' => 'lonja', 'Lj9A510G79' => 'lonja', 'Lsat_1_v5_gn_1_34781' => 'lsa', 'Lsat_1_v5_gn_1_95220' => 'lsa', 'Lsat_1_v5_gn_3_107940' => 'lsa', 'Lsat_1_v5_gn_3_107960' => 'lsa', 'Lsat_1_v5_gn_5_89141' => 'lsa', 'Lsat_1_v5_gn_6_14841' => 'lsa', 'Lsat_1_v5_gn_8_62840' => 'lsa', 'Lsat_1_v5_gn_8_84480' => 'lsa', 'Lsat_1_v5_gn_8_96380' => 'lsa', 'Manes.03G187800' => 'mes', 'Manes.11G036600' => 'mes', 'Manes.15G020300' => 'mes', 'Manes.16G111900' => 'mes', 'Mapoly0030s0069' => 'mpo', 'Mapoly0110s0022' => 'mpo', 'Mapoly0116s0039' => 'mpo', 'Mapoly0129s0023' => 'mpo', 'MBI01_g06185_MAGBIO' => 'mbi', 'MCO04G061' => 'mco', 'MCO06G129' => 'mco', 'MCO07G385' => 'mco', 'MCO16G578' => 'mco', 'MD02G1058500' => 'mdo', 'MD13G1178700' => 'mdo', 'MD15G1192800' => 'mdo', 'MD16G1179900' => 'mdo', 'MD17G1188900' => 'mdo', 'Medtr2g020970' => 'mtr', 'Medtr2g101350' => 'mtr', 'Medtr4g118340' => 'mtr', 'Medtr6g087000' => 'mtr', 'Medtr8g033020' => 'mtr', 'MELO3C006581.2' => 'cme', 'MELO3C021385.2' => 'cme', 'MELO3C024262.2' => 'cme', 'MELO3C024635.2' => 'cme', 'Migut.G00279' => 'egut', 'Migut.G00287' => 'egut', 'Migut.I00929' => 'egut', 'Migut.K00517' => 'egut', 'MSTRG.10027' => 'ama', 'MSTRG.11044' => 'ama', 'MSTRG.26370' => 'ama', 'MSTRG.3974' => 'ama', 'Nitab4.5_0000010g0080' => 'nta', 'Nitab4.5_0000059g0180' => 'nta', 'Nitab4.5_0000568g0100' => 'nta', 'Nitab4.5_0000568g0110' => 'nta', 'Nitab4.5_0000568g0120' => 'nta', 'Nitab4.5_0000952g0070' => 'nta', 'Nitab4.5_0001591g0200' => 'nta', 'Nitab4.5_0006985g0030' => 'nta', 'Nitab4.5_0008532g0010' => 'nta', 'Nitab4.5_0011578g0030' => 'nta', 'Nitab4.5_0021337g0010' => 'nta', 'Nn2g11646' => 'nnu', 'Nn3g18153' => 'nnu', 'Nn3g21172' => 'nnu', 'Nn3g21173' => 'nnu', 'Nn4g26124' => 'nnu', 'Oeu017817.1' => 'oeu', 'Oeu026083.1' => 'oeu', 'Oeu026084.1' => 'oeu', 'Oeu029295.3' => 'oeu', 'Oeu037985.1' => 'oeu', 'Oeu044813.1' => 'oeu', 'Os01g0231800' => 'osa', 'Os01g0231900' => 'osa', 'Os02g0281000' => 'osa', 'Os07g0646100' => 'osa', 'Peaxi162Scf00015g00128' => 'pax', 'Peaxi162Scf00095g00528' => 'pax', 'Peaxi162Scf00539g00036' => 'pax', 'PGR102G2383' => 'pgr', 'PGR142G4412' => 'pgr', 'PGSC0003DMG400001428' => 'stu', 'PGSC0003DMG400032110' => 'stu', 'PGSC0003DMG401002551' => 'stu', 'Phvul.003G098000' => 'pvu', 'Phvul.004G169300' => 'pvu', 'Phvul.005G170400' => 'pvu', 'Phvul.006G157900' => 'pvu', 'Potri.001G186600' => 'ptr', 'Potri.008G198700' => 'ptr', 'Potri.010G028300' => 'ptr', 'Potri.018G084900' => 'ptr', 'Pp3c16_10470' => 'ppa', 'Pp3c16_18360' => 'ppa', 'Pp3c21_4790' => 'ppa', 'Pp3c22_7030' => 'ppa', 'Pp3c25_7050' => 'ppa', 'Pp3c2_4410' => 'ppa', 'PRCOL_00001011' => 'pco', 'PRCOL_00002746' => 'pco', 'PRCOL_00004954' => 'pco', 'PRCOL_00006801' => 'pco', 'Prupe.1G147500' => 'ppe', 'Prupe.3G063900' => 'ppe', 'Prupe.7G224500' => 'ppe', 'Psat0ss7919g0120' => 'psa', 'Psat1g005440' => 'psa', 'Psat1g045440' => 'psa', 'Psat1g156000' => 'psa', 'Psat1g185400' => 'psa', 'PSO170G3874' => 'pso', 'PSO210G1626' => 'pso', 'PSO210G3200' => 'pso', 'PSO210G3424' => 'pso', 'PSO302G0301' => 'pso', 'PSO566G0332' => 'pso', 'PSO782G2586' => 'pso', 'QL02p043064' => 'qlo', 'QL05p021219' => 'qlo', 'QL05p021238' => 'qlo', 'QL05p021244' => 'qlo', 'QL06p006161' => 'qlo', 'RcHm_v2.0_Chr2g0091381' => 'rch', 'RcHm_v2.0_Chr2g0139461' => 'rch', 'RcHm_v2.0_Chr4g0419711' => 'rch', 'Rhsim04G0213000' => 'rsi', 'Rhsim05G0043400' => 'rsi', 'Rhsim12G0201500' => 'rsi', 'Sabra01G0153700' => 'sbr', 'Sabra08G0161900' => 'sbr', 'Sabra10G0012500' => 'sbr', 'Sabra18G0073300' => 'sbr', 'SalBow2G1883' => 'sbo', 'SalBow5G1246' => 'sbo', 'SalBow5G1616' => 'sbo', 'Sc10g0007280' => 'sci', 'Sc13g0003800' => 'sci', 'Sc14g0000410' => 'sci', 'Sc25g0004520' => 'sci', 'Sc25g0004530' => 'sci', 'Sed0007714' => 'sed', 'Sed0008742' => 'sed', 'Sed0021399' => 'sed', 'Sed0023246' => 'sed', 'Sed0028015' => 'sed', 'SEGI_15304' => 'sgi', 'SEGI_17721' => 'sgi', 'SEGI_23538' => 'sgi', 'SEGI_36398' => 'sgi', 'SEGI_40800' => 'sgi', 'SGA_v2.0_scaffold142G35636' => 'sas', 'SGA_v2.0_scaffold19G08755' => 'sas', 'SGA_v2.0_scaffold237G43851' => 'sas', 'SGA_v2.0_scaffold36G14440' => 'sas', 'SGA_v2.0_scaffold5G02539' => 'sas', 'SHI00348' => 'shi', 'SHI11057' => 'shi', 'SHI11058' => 'shi', 'SHI11059' => 'shi', 'SHI11060' => 'shi', 'SMO119G0320' => 'smo', 'SMO146G0147' => 'smo', 'SMO172G0193' => 'smo', 'SMO340G0259' => 'smo', 'Solyc01g080400.3' => 'sly', 'Solyc02g088200.4' => 'sly', 'Solyc03g120480.3' => 'sly', 'Solyc05g018300.3' => 'sly', 'Sopen01g032210' => 'spe', 'Sopen02g032890' => 'spe', 'Sopen03g039360' => 'spe', 'Sopen05g015040' => 'spe', 'Sp3g05190' => 'spa', 'Sp3g14590' => 'spa', 'Sp3g14600' => 'spa', 'Sp3g33360' => 'spa', 'TAR365G0525' => 'tar', 'TAR383G0250' => 'tar', 'TAR383G0479' => 'tar', 'TAR636G1889' => 'tar', 'THA.LOC104802736' => 'tha', 'THA.LOC104804013' => 'tha', 'THA.LOC104817973' => 'tha', 'THA.LOC104818829' => 'tha', 'Thecc.04G271900' => 'tca', 'Thecc.06G095300' => 'tca', 'Thecc.09G104600' => 'tca', 'Thhalv10001889m.g' => 'esa', 'Thhalv10020736m.g' => 'esa', 'Thhalv10021055m.g' => 'esa', 'Thhalv10021339m.g' => 'esa', 'TPR.G28129' => 'tpr', 'TPR.G28826' => 'tpr', 'TPR.G37234' => 'tpr', 'TWI09G0880' => 'twi', 'TWI12G1071' => 'twi', 'TWI34G0335' => 'twi', 'unitig_22.g6211' => 'ugi', 'unitig_22.g6212' => 'ugi', 'unitig_32.g11743' => 'ugi', 'vmacro08243' => 'vma', 'vmacro10875' => 'vma', 'vmacro16977' => 'vma', 'VMungo0464G0217' => 'vmu', 'VMungo0540G0073' => 'vmu', 'VMungo1080G1628' => 'vmu', 'Zm00001eb110450' => 'zma', 'Zm00001eb119210' => 'zma', 'Zm00001eb203570' => 'zma', 'Zm00001eb329360' => 'zma' ) $gf_id = 'HOM05D001353' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001353' ) $data_identifier = 'HOM05D001353' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 3, 'aag' => (int) 4, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 5, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 5, 'acertr' => (int) 4, 'cqu' => (int) 6, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 3, 'din' => (int) 4, 'dzi' => (int) 4, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 4, 'vpl' => (int) 6, 'sun' => (int) 2, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 9, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 1, 'mco' => (int) 4, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 3, 'pgr' => (int) 2, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 6, 'pco' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 5, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb329360' $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